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- PDB-5xte: Cryo-EM structure of human respiratory complex III (cytochrome bc... -

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Entry
Database: PDB / ID: 5xte
TitleCryo-EM structure of human respiratory complex III (cytochrome bc1 complex)
Components
  • (Cytochrome b-c1 complex subunit ...) x 9
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial
KeywordsOXIDOREDUCTASE/ELECTRON TRANSPORT / Respiratory / OXIDOREDUCTASE-ELECTRON TRANSPORT complex
Function / homologyCytochrome c1 / Cytochrome b-c1 complex subunit 10 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 7 superfamily / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b / Single alpha-helix domain superfamily / Cytochrome b/b6-like domain superfamily / Ubiquinol-cytochrome C reductase hinge domain ...Cytochrome c1 / Cytochrome b-c1 complex subunit 10 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 7 superfamily / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b / Single alpha-helix domain superfamily / Cytochrome b/b6-like domain superfamily / Ubiquinol-cytochrome C reductase hinge domain / Cytochrome c1, transmembrane anchor, C-terminal / Rieske [2Fe-2S] iron-sulphur domain / Di-haem cytochrome, transmembrane / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Rieske iron-sulphur protein / Cytochrome c-like domain superfamily / Peptidase M16, N-terminal / Metalloenzyme, LuxS/M16 peptidase-like / Globular protein, non-globular alpha/beta subunit / Cytochrome b-c1 complex subunit 9 / Peptidase M16, C-terminal / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, C-terminal / Peptidase M16, zinc-binding site / Cytochrome b/b6, N-terminal / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex, subunit 6 / Ubiquinol-cytochrome C reductase hinge domain superfamily / Cytochrome b-c1 complex subunit 9 superfamily / Rieske [2Fe-2S] iron-sulphur domain superfamily / Ubiquinol cytochrome reductase transmembrane region / Respiratory electron transport / Mitochondrial protein import / Rieske [2Fe-2S] iron-sulfur domain profile. / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6 N-terminal region profile. / Insulinase family, zinc-binding region signature. / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Peptidase M16 inactive domain / UcrQ family / Ubiquinol-cytochrome C reductase hinge protein / Insulinase (Peptidase family M16) / Cytochrome b-c1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6/petB / Rieske [2Fe-2S] domain / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Cytochrome C1 family / Ubiquinol-cytochrome C reductase complex 14kD subunit / hyperosmotic salinity response / protein processing involved in protein targeting to mitochondrion / subthalamus development / pons development / mitochondrial respiratory chain complex III assembly / response to alkaloid / electron transporter, transferring electrons within CoQH2-cytochrome c reductase complex activity / response to mercury ion / cerebellar Purkinje cell layer development / mitochondrial respiratory chain complex III / mitochondrial respiratory chain / oxidative phosphorylation / ubiquinol—cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial ATP synthesis coupled proton transport / electron transporter, transferring electrons from CoQH2-cytochrome c reductase complex and cytochrome c oxidase complex activity / integral component of mitochondrial inner membrane / mitochondrial respiratory chain complex IV / thalamus development / pyramidal neuron development / hypothalamus development / response to hormone / response to glucagon / mitochondrial electron transport, ubiquinol to cytochrome c / response to cobalamin / midbrain development / response to copper ion / aerobic respiration / respiratory chain / response to hyperoxia / hippocampus development / protein processing / response to activity / generation of precursor metabolites and energy / 2 iron, 2 sulfur cluster binding / response to calcium ion / animal organ regeneration / metalloendopeptidase activity / mitochondrial inner membrane / response to heat / response to cadmium ion / oxidation-reduction process / response to ethanol / response to hypoxia / electron transfer activity / response to drug / myelin sheath / response to antibiotic
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.4 Å resolution
AuthorsGu, J. / Wu, M. / Yang, M.
CitationJournal: Cell / Year: 2017
Title: Architecture of Human Mitochondrial Respiratory Megacomplex IIIIIV.
Authors: Runyu Guo / Shuai Zong / Meng Wu / Jinke Gu / Maojun Yang
Abstract: The respiratory megacomplex represents the highest-order assembly of respiratory chain complexes, and it allows mitochondria to respond to energy-requiring conditions. To understand its architecture, ...The respiratory megacomplex represents the highest-order assembly of respiratory chain complexes, and it allows mitochondria to respond to energy-requiring conditions. To understand its architecture, we examined the human respiratory chain megacomplex-IIIIIV (MCIIIIIV) with 140 subunits and a subset of associated cofactors using cryo-electron microscopy. The MCIIIIIV forms a circular structure with the dimeric CIII located in the center, where it is surrounded by two copies each of CI and CIV. Two cytochrome c (Cyt.c) molecules are positioned to accept electrons on the surface of the c state CIII dimer. Analyses indicate that CII could insert into the gaps between CI and CIV to form a closed ring, which we termed the electron transport chain supercomplex. The structure not only reveals the precise assignment of individual subunits of human CI and CIII, but also enables future in-depth analysis of the electron transport chain as a whole.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 19, 2017 / Release: Aug 30, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 30, 2017Structure modelrepositoryInitial release
1.1Sep 6, 2017Structure modelDatabase referencescitation_citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
1.2Dec 6, 2017Structure modelData processing / Database referencescitation / em_software_citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_software.name

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Assembly

Deposited unit
A: Cytochrome b-c1 complex subunit 8
B: Cytochrome b-c1 complex subunit Rieske, mitochondrial
C: Cytochrome b-c1 complex subunit Rieske, mitochondrial
D: Cytochrome b-c1 complex subunit 9
E: Cytochrome b-c1 complex subunit 6, mitochondrial
F: Cytochrome b-c1 complex subunit 7
G: Cytochrome b-c1 complex subunit 10
H: Cytochrome c1, heme protein, mitochondrial
J: Cytochrome b
K: Cytochrome b-c1 complex subunit 2, mitochondrial
L: Cytochrome b-c1 complex subunit 1, mitochondrial
N: Cytochrome b-c1 complex subunit 8
O: Cytochrome b-c1 complex subunit Rieske, mitochondrial
P: Cytochrome b-c1 complex subunit Rieske, mitochondrial
Q: Cytochrome b-c1 complex subunit 9
R: Cytochrome b-c1 complex subunit 6, mitochondrial
S: Cytochrome b-c1 complex subunit 7
T: Cytochrome b-c1 complex subunit 10
U: Cytochrome c1, heme protein, mitochondrial
V: Cytochrome b
W: Cytochrome b-c1 complex subunit 2, mitochondrial
Y: Cytochrome b-c1 complex subunit 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)497,16148
Polyers473,13422
Non-polymers24,02726
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)122840
ΔGint (kcal/M)-879
Surface area (Å2)163400

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Components

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Cytochrome b-c1 complex subunit ... , 9 types, 18 molecules ANBOCPDQERFSGTKWLY

#1: Protein/peptide Cytochrome b-c1 complex subunit 8 / Complex III subunit 8 / Complex III subunit VIII / Ubiquinol-cytochrome c reductase complex 9.5 kDa protein / Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C


Mass: 9791.181 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: O14949
#2: Protein/peptide Cytochrome b-c1 complex subunit Rieske, mitochondrial / Complex III subunit 5 / Cytochrome b-c1 complex subunit 5 / Rieske iron-sulfur protein / RISP / Ubiquinol-cytochrome c reductase iron-sulfur subunit


Mass: 5893.814 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-57 / Source: (natural) Homo sapiens (human)
References: UniProt: P47985, ubiquinol—cytochrome-c reductase
#3: Protein/peptide Cytochrome b-c1 complex subunit Rieske, mitochondrial / Complex III subunit 5 / Cytochrome b-c1 complex subunit 5 / Rieske iron-sulfur protein / RISP / Ubiquinol-cytochrome c reductase iron-sulfur subunit


Mass: 21645.578 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human)
References: UniProt: P47985, ubiquinol—cytochrome-c reductase
#4: Protein/peptide Cytochrome b-c1 complex subunit 9 / Complex III subunit 9 / Complex III subunit X / Cytochrome c1 non-heme 7 kDa protein / Ubiquinol-cytochrome c reductase complex 7.2 kDa protein


Mass: 7189.299 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UDW1
#5: Protein/peptide Cytochrome b-c1 complex subunit 6, mitochondrial / Complex III subunit 6 / Complex III subunit VIII / Cytochrome c1 non-heme 11 kDa protein / Mitochondrial hinge protein / Ubiquinol-cytochrome c reductase complex 11 kDa protein


Mass: 8990.854 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: P07919
#6: Protein/peptide Cytochrome b-c1 complex subunit 7 / Complex III subunit 7 / Complex III subunit VII / QP-C / Ubiquinol-cytochrome c reductase complex 14 kDa protein


Mass: 13037.842 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 6-111 / Source: (natural) Homo sapiens (human) / References: UniProt: P14927
#7: Protein/peptide Cytochrome b-c1 complex subunit 10 / Complex III subunit 10 / Complex III subunit XI / Ubiquinol-cytochrome c reductase complex 6.4 kDa protein


Mass: 5958.912 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2-52 / Source: (natural) Homo sapiens (human) / References: UniProt: O14957
#10: Protein/peptide Cytochrome b-c1 complex subunit 2, mitochondrial / Complex III subunit 2 / Core protein II / Ubiquinol-cytochrome-c reductase complex core protein 2


Mass: 44946.582 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 35-453 / Source: (natural) Homo sapiens (human) / References: UniProt: P22695
#11: Protein/peptide Cytochrome b-c1 complex subunit 1, mitochondrial / Complex III subunit 1 / Core protein I / Ubiquinol-cytochrome-c reductase complex core protein 1


Mass: 49181.430 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: P31930

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Protein/peptide , 2 types, 4 molecules HUJV

#8: Protein/peptide Cytochrome c1, heme protein, mitochondrial / / Complex III subunit 4 / Complex III subunit IV / Cytochrome b-c1 complex subunit 4 / Ubiquinol-cytochrome-c reductase complex cytochrome c1 subunit / Cytochrome c-1


Mass: 27388.395 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: P08574
#9: Protein/peptide Cytochrome b / / Complex III subunit 3 / Complex III subunit III / Cytochrome b-c1 complex subunit 3 / Ubiquinol-cytochrome-c reductase complex cytochrome b subunit


Mass: 42543.016 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: P00156

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Non-polymers , 6 types, 26 molecules

#12: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 9 / Formula: C81H156O17P2 / Cardiolipin / Comment: phospholipid *YM
#13: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Formula: Fe2S2
#14: Chemical
ChemComp-PEE / 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 749.073 Da / Num. of mol.: 6 / Formula: C41H83NO8P / Discrete optimized protein energy / Comment: DOPE (phospholipid) *YM
#15: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Formula: C34H34FeN4O4 / Heme C
#16: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Formula: C34H32FeN4O4 / Heme
#17: Chemical ChemComp-PLX / (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL


Mass: 767.132 Da / Num. of mol.: 3 / Formula: C42H89NO8P

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human respiratory complex III (cytochrome bc1 complex)
Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.25 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1EMAN2.1particle selection
2AutoEMation2.0image acquisition
4CTFFIND3.0CTF correction
7Coot0.8.2model fitting
9RELION1.4initial Euler assignment
10RELION1.4final Euler assignment
11RELION1.4classification
12RELION1.43D reconstruction
13PHENIX1.11.1model refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 167761 / Symmetry type: POINT

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